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Targeted Capture and Massively Parallel Sequencing of 12 Human Exomes

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Targeted Capture and Massively Parallel Sequencing of 12 Human Exomes Vol 461 | 10 September 2009 | doi:10.1038/nature08250 LETTERS Targeted capture and massively parallel sequencing of 12 human exomes Sarah B. Ng1, Emily H. Turner1, Peggy D. Robertson1, Steven D. Flygare1, Abigail W. Bigham2, Choli Lee1, Tristan Shaffer1, Michelle Wong1, Arindam Bhattacharjee4, Evan E. Eichler1,3, Michael Bamshad2, Deborah A. Nickerson1 & Jay Shendure1 Genome-wide association studies suggest that common genetic mutations in MYH3 (ref. 5). Unpaired, 76 base-pair (bp) reads12 variants explain only a modest fraction of heritable risk for com- from post-enrichment shotgun libraries were aligned to the reference mon diseases, raising the question of whether rare variants account genome13. On average, 6.4 gigabases (Gb) of mappable sequence was for a significant fraction of unexplained heritability1,2. Although generated per individual (20-fold less than whole genome sequencing DNA sequencing costs have fallen markedly3,theyremainfarfrom with the same platform12), and 49% of reads mapped to targets what is necessary for rare and novel variants to be routinely iden- (Supplementary Table 1). After removing duplicate reads that tified at a genome-wide scale in large cohorts. We have therefore represent potential polymerase chain reaction artefacts14, the average sought to develop second-generation methods for targeted sequen- fold-coverage of each exome was 513 (Supplementary Fig. 1). On cing of all protein-coding regions (‘exomes’), to reduce costs while average per exome, 99.7% of targeted bases were covered at least enriching for discovery of highly penetrant variants. Here we report once, and 96.3% (25.6 Mb) were covered sufficiently for variant call- on the targeted capture and massively parallel sequencing of the ing ($83 coverage and Phred-like15 consensus quality $30). This exomes of 12 humans. These include eight HapMap individuals corresponded to 78% of genes having .95% of their coding bases representing three populations4, and four unrelated individuals called (Supplementary Fig. 2 and Supplementary Data 2). The aver- with a rare dominantly inherited disorder, Freeman–Sheldon syn- age pairwise correlation coefficient between individuals for gene-by- drome (FSS)5. We demonstrate the sensitive and specific identifica- gene coverage was 0.87, consistent with systematic bias in coverage tion of rare and common variants in over 300 megabases of coding between individual exomes. sequence. Using FSS as a proof-of-concept, we show that candidate False positives and false negatives are critical issues in genomic genes for Mendelian disorders can be identified by exome sequen- resequencing. We assessed the quality of our exome data in four ways. cing of a small number of unrelated, affected individuals. This First, comparing sequence-based calls for the eight HapMap exomes strategy may be extendable to diseases with more complex genetics to array-based genotyping, we observed a high concordance with through larger sample sizes and appropriate weighting of non- both homozygous (99.94%; n 5 219,077) and heterozygous synonymous variants by predicted functional impact. (99.57%; n 5 43,070) genotypes (Table 1). Second, we compared Protein-coding regions constitute ,1% of the human genome or our coding single-nucleotide polymorphism (cSNP) catalogue to ,30 megabases (Mb), split across ,180,000 exons. A brute-force ,1 Mb of coding sequence determined in each of the eight approach to exome sequencing with conventional technology6 is HapMap individuals by molecular inversion probe (MIP) capture expensive relative to what may be possible with second-generation and direct resequencing16. At coordinates called in both data sets, platforms3. However, the efficient isolation of this fragmentary geno- 99.9% of all cSNPs (n 5 4,620) and 100% of novel cSNPs mic subset is technically challenging7. The enrichment of an exome (n 5 334) identified here were concordant, consistent with a low false by hybridization of shotgun libraries constructed from 140 mgof discovery rate. Third, we compared the NA18507 cSNPs identified genomic DNA to seven microarrays was described previously8.To here to those called by recent whole genome sequencing of this improve the practicality of hybridization capture, we developed a individual12, and found substantial overlap (Supplementary Fig. 3). protocol to enrich for coding sequences at a genome-wide scale start- The relative numbers of cSNPs called by only one approach, and the ing with 10 mg of DNA and using two microarrays. Our initial target proportions of these represented in dbSNP, indicate that exome was 27.9 Mb of coding sequence defined by CCDS (the NCBI sequencing has equivalent sensitivity for cSNP detection compared Consensus Coding Sequence database)9. This curated set avoids the to whole genome sequencing. Fourth, we compared our data to inclusion of spurious hypothetical genes that contaminate broader cSNPs in high-quality Sanger sequence of single haplotype regions exome definitions10. The target is reduced to 26.6 Mb on exclusion of from fosmid clones of the same HapMap individuals17. Most fosmid- regions that are poorly mapped with our anticipated read length defined cSNPs (38 of 40) were at coordinates with sufficient coverage owing to paralogous sequences elsewhere in the genome in our data for variant calling. Of these, 38 of 38 were correctly (Supplementary Data 1). identified as variant. We captured and sequenced the exomes of eight individuals previ- A comparison of our data to past reports on exonic18 or exomic8 ously characterized by the HapMap4 and Human Genome Structural array-based capture revealed roughly equivalent capture specificity, Variation11 projects. We also analysed four unrelated individuals but greater completeness in terms of coverage and variant calling affected with Freeman–Sheldon syndrome (FSS; Online Mendelian (Supplementary Table 2). These improvements probably arise from Inheritance in Man (OMIM) #193700), also called distal arthro- a combination of greater sequencing depth and differences in array gryposis type 2A, a rare autosomal dominant disorder caused by designs and in experimental conditions for capture. Within the set of 1Department of Genome Sciences, 2Department of Pediatrics, University of Washington, 3Howard Hughes Medical Institute, Seattle, Washington 98195, USA. 4Agilent Technologies, Santa Clara, California 95051, USA. 272 ©2009 Macmillan Publishers Limited. All rights reserved NATURE | Vol 461 | 10 September 2009 LETTERS Table 1 | Sequence coverage and array-based validation Concordance with Illumina Human1M-Duo calls Individual Covered $13 Sequence called Homozygous reference Heterozygous Homozygous non-reference NA18507 (YRI) 26,477,161 (99.7%) 25,795,189 (97.1%) 23757/23762 (99.98%) 5553/5583 (99.46%) 3582/3592 (99.72%) NA18517 (YRI) 26,476,761 (99.7%) 25,748,289 (97.0%) 23701/23705 (99.98%) 5575/5601 (99.54%) 3568/3579 (99.69%) NA19129 (YRI) 26,491,035 (99.8%) 25,733,587 (96.9%) 23701/23708 (99.97%) 5482/5510 (99.49%) 3681/3690 (99.76%) NA19240 (YRI) 26,486,481 (99.7%) 25,576,517 (96.3%) 23546/23551 (99.98%) 5600/5634 (99.40%) 3542/3549 (99.80%) NA18555 (CHB) 26,475,665 (99.7%) 25,529,861 (96.1%) 23980/23984 (99.98%) 4877/4893 (99.67%) 3776/3786 (99.74%) NA18956 (JPT) 26,454,942 (99.6%) 25,683,248 (96.7%) 24217/24221 (99.98%) 4890/4910 (99.59%) 3751/3760 (99.76%) NA12156 (CEU) 26,476,155 (99.7%) 25,360,704 (95.5%) 23789/23794 (99.98%) 5493/5514 (99.62%) 3206/3213 (99.78%) NA12878 (CEU) 26,439,953 (99.6%) 25,399,572 (95.6%) 23885/23891 (99.97%) 5413/5425 (99.78%) 3274/3292 (99.45%) FSS10066 (Eur) 26,467,140 (99.7%) 25,546,738 (96.2%) NA NA NA FSS10208 (Eur) 26,461,768 (99.6%) 25,576,256 (96.3%) NA NA NA FSS22194 (Eur) 26,426,401 (99.5%) 25,454,551 (95.9%) NA NA NA FSS24895 (Eur) 26,478,775 (99.7%) 25,602,677 (96.4%) NA NA NA The number of coding bases covered at least 13 and with sufficient coverage to variant call ($83 and consensus quality $30) are listed for each exome, with the fraction of the aggregate target (26.6 Mb) that this represents in parentheses. For the eight HapMap individuals, concordance with array genotyping (Illumina Human1M-Duo) is listed for positions that are homozygous for the reference allele, heterozygous or homozygous for the non-reference allele (according to the array genotype). CEU, CEPH HapMap; CHB, Chinese HapMap; Eur, European–American ancestry (non- HapMap); JPT, Japanese HapMap; YRI, Yoruba HapMap. NA, Not applicable. called positions, the high concordance with heterozygous array- (n 5 47,079), 32% of annotated variants and 86% of novel variants based genotypes (.99%) provides an estimate of our sensitivity for were singleton observations across 24 chromosomes (Fig. 1a). rare variant detection, as rare variants are overwhelmingly expected We also estimated the total number of cSNPs in each individual to be heterozygous. However, sensitivity was limited in that ,4% of relative to the reference genome (Table 2b). As the precise and com- known heterozygous genotypes were at coordinates where there was prehensive definition of the human exome remains incomplete, we insufficient coverage to make a confident call. extrapolated our data to an estimated exome size of exactly 30 Mb. There were 56,240 cSNPs called in one or more individuals, of The results were remarkably consistent by population. As expected, a which 13,347 were novel. On average, 17,272 cSNPs were called per higher number of non-synonymous cSNPs were estimated for the individual, of which 92% were already annotated in a public database Yoruba individuals (average 10,254; n 5 4) than non-Africans (aver- (dbSNP v129) (Table 2a). The proportion of previously annotated age 8,489; n 5 8). More heterozygous cSNPs were estimated for the cSNPs was consistent by population, and higher for European (94%; four Yoruba (average 14,995) than the six European Americans n 5 6) and Asian (93%; n 5 2) than Yoruba (88%; n 5 4) ancestry.
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